Fluorescence - Detector Offsets¶
allows for correction of small offsets in the measurements caused by actinic light current/ground loop on main and addon boards
Used with Bleed CAL#7B
These calibration steps require the chlorophyll calibration and the pink fluorescent cards
2231
Basic Usage¶
## Import fluorescence_detector_offsets_calibration
from jii_multispeq_protocols.protocols.calibrations import fluorescence_detector_offsets_calibration as _fluorescence_detector_offsets_calibration
Sequence¶
%%{
init: {
"theme": "base",
"themeVariables": {"primaryColor": "#49e06d", "primaryTextColor": "#005e5e", "primaryBorderColor": "#005e5e", "lineColor": "#fff381", "secondaryColor": "#afd7f4", "tertiaryColor": "#D7EBF9"}
}
}%%
flowchart TD
START((Start))
A0["`**Protocol**
Runs only during *first* repeat`"]:::protocol
START ==> A0
A1["`**bc1**
*Detector:*
• 700nm - 1150nm
• 400nm - 700nm (BG18)
*Pulsed LEDs:*
• 530nm (Main)
• 590nm (Main)
• 950nm (Clamp)
• 820nm (Clamp)
*Non Pulsed LED:* `"]:::protocol
A0 ==>|"`**Illumination**
655nm (Main)
*Duration (ms)*: 0
*PAR*: 200`"| A1
A2["`**bc0**
*Detector:*
• 700nm - 1150nm
• 400nm - 700nm (BG18)
*Pulsed LEDs:*
• 530nm (Main)
• 590nm (Main)
• 950nm (Clamp)
• 820nm (Clamp)
*Non Pulsed LED:* `"]:::protocol
A1 ==>|"`**Illumination**
655nm (Main)
*Duration (ms)*: 0
*PAR*: 200`"| A2
A2 ==> END
A2 -.-> |2x| A0
linkStyle 4 stroke-width:3px
END(( End ))
classDef protocol text-align:left,white-space:pre;
Details¶
Code¶
[ { '_protocol_set_': [ { 'alert': 'Clamp the Fluorescent Card (pink)',
'autogain': [ [1, 1, 3, 15, 50000],
[6, 6, 1, 15, 50000],
[0, 10, 1, 15, 50000]],
'do_once': 1},
{ 'bleed_correction': 1,
'detectors': [ [3, 1, 1, 1],
[3, 1, 1, 1],
[3, 1, 1, 1]],
'label': 'bc1',
'nonpulsed_lights': [['@s2'], ['@s2'], ['@s2']],
'nonpulsed_lights_brightness': [ [0],
['@p0'],
[0]],
'pre_illumination': [2, 0, '@n1:0'],
'protocol_averages': 1,
'protocol_repeats': '#l0',
'pulse_distance': [2000, 2000, 2000],
'pulse_length': [ ['a_d1', 'a_d6', 'a_d0', 20],
['a_d1', 'a_d6', 'a_d0', 20],
['a_d1', 'a_d6', 'a_d0', 20]],
'pulsed_lights': [ [1, 6, 10, 3],
[1, 6, 10, 3],
[1, 6, 10, 3]],
'pulsed_lights_brightness': [ [ 'a_b1',
'a_b6',
'a_b0',
400],
[ 'a_b1',
'a_b6',
'a_b0',
400],
[ 'a_b1',
'a_b6',
'a_b0',
400]],
'pulses': ['@n1:1', '@n1:1', '@n1:1'],
'pulses_delay': [1, 1, 1]},
{ 'bleed_correction': 0,
'detectors': [ [3, 1, 1, 1],
[3, 1, 1, 1],
[3, 1, 1, 1]],
'label': 'bc0',
'nonpulsed_lights': [['@s2'], ['@s2'], ['@s2']],
'nonpulsed_lights_brightness': [ [0],
['@p0'],
[0]],
'pre_illumination': [2, 0, '@n1:0'],
'protocol_averages': 1,
'protocol_repeats': '#l0',
'pulse_distance': [2000, 2000, 2000],
'pulse_length': [ ['a_d1', 'a_d6', 'a_d0', 20],
['a_d1', 'a_d6', 'a_d0', 20],
['a_d1', 'a_d6', 'a_d0', 20]],
'pulsed_lights': [ [1, 6, 10, 3],
[1, 6, 10, 3],
[1, 6, 10, 3]],
'pulsed_lights_brightness': [ [ 'a_b1',
'a_b6',
'a_b0',
400],
[ 'a_b1',
'a_b6',
'a_b0',
400],
[ 'a_b1',
'a_b6',
'a_b0',
400]],
'pulses': ['@n1:1', '@n1:1', '@n1:1'],
'pulses_delay': [1, 1, 1]}],
'set_repeats': '#l2',
'v_arrays': [ [0, -200, -400, -750, -1000, -2000, -3000, -4000],
[200, 30],
[2, 9],
[1, 0, 1, 0]]}]
Analysis¶
Usage¶
JII-MultispeQ package)¶from jii_multispeq import measurement as _measurement
from jii_multispeq_protocols.protocols.calibrations import fluorescence_detector_offsets_calibration as _fluorescence_detector_offsets_calibration
## Take a measurement using the MultispeQ
data, crc32 = _measurement.measure(port="<Selected Port>", protocol=_fluorescence_detector_offsets_calibration, filename=None, notes="")
## The analyze function of JII-MultispeQ helps to provide the correct format
output = _measurement.analyze( data, _fluorescence_detector_offsets_calibration._analyze )
## View Analysis output (as table)
_measurement.view( output )
Function Details¶
- _analyze(_data)[source]
Macro for data evaluation artifacts on measurements caused by actinic light ground loops data on PhotosynQ.org by: David M. Kramer created: 2017-05-09 @ 18:15:27
Example Data¶
Parameter |
Value |
|---|---|
device_battery |
98 |
device_firmware |
2.343 |
device_id |
52:00:12:bc |
device_name |
MultispeQ |
device_version |
2 |
status |
Test OK |
toDevice |
bleed3+0+0+0+0+0+0+0+0+0+bleed3+1+0+0+0+0+0+0+0+0+bleed3+2+0+0+0+0+0+0+0+0+bleed3+3+0+0+0+0+0+0+0+0+bleed3+4+0+0+0+0+0+0+0+0+bleed3+5+0+0+0+0+0+0+0+0+bleed3+6+0+0+0+0+0+0+0+0+bleed3+7+0+0+0+0+0+0+0+0+bleed3+8+0+0+0+0+0+0+0+0+bleed3+9+0+0+0+0+0+0+0+0+bleed3+10+0+0+0+0+0+0+0+0+bleed3+11+0+0+0+0+0+0+0+0+bleed3+12+0+0+0+0+0+0+0+0+bleed3+13+0+0+0+0+0+0+0+0+bleed3+14+0+0+0+0+0+0+0+0+bleed3+1+-36.0+201.0+272.0+359.0+418.0+483.0+638.0+745.0+bleed3+3+-6.0+4.0+16.0+28.0+38.0+68.0+116.0+181.0+bleed3+7+-38.0+24.0+5.0+3.0+32.0+62.0+42.0+90.0+bleed3+2+0.0+2.0+1.0+-5.0+-16.0+-27.0+-47.0+-57.0+bleed3+14+-18.0+69.0+182.0+268.0+309.0+548.0+782.0+926.0+bleed3+10+-4.0+94.0+398.0+991.0+1402.0+3018.0+4581.0+6064.0+bleed3+13+-19.0+8.0+41.0+128.0+183.0+452.0+644.0+820.0+bleed3+8+1.0+4.0+10.0+0.0+12.0+19.0+32.0+47.0+setCalTime+2+setCalOK+2+0+ |